One rumor going around is that the Federation finds Khans ship the 'Botany Bay'. Spock 'prime' already knows what could happen and it is decided that Khan must die. Cumberbatch is Khan's second in command and seeks vengeance.

Again... just a theory.

That would suck, as it would reduce Khan to nothing more than a quick blip in this particular Star Trek universe. Would rather just have Cumberbatch be Khan. Will be interesting to see.